Job ID = 12531696 SRX = SRX4555065 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8399561 spots for SRR7696768/SRR7696768.sra Written 8399561 spots for SRR7696768/SRR7696768.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:49 8399561 reads; of these: 8399561 (100.00%) were paired; of these: 453501 (5.40%) aligned concordantly 0 times 4250590 (50.60%) aligned concordantly exactly 1 time 3695470 (44.00%) aligned concordantly >1 times ---- 453501 pairs aligned concordantly 0 times; of these: 32591 (7.19%) aligned discordantly 1 time ---- 420910 pairs aligned 0 times concordantly or discordantly; of these: 841820 mates make up the pairs; of these: 671966 (79.82%) aligned 0 times 85281 (10.13%) aligned exactly 1 time 84573 (10.05%) aligned >1 times 96.00% overall alignment rate Time searching: 00:10:49 Overall time: 00:10:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 1280226 / 3629906 = 0.3527 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:28:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 17 Apr 2021 09:28:48: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:28:48: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:28:54: 1000000 INFO @ Sat, 17 Apr 2021 09:29:00: 2000000 INFO @ Sat, 17 Apr 2021 09:29:06: 3000000 INFO @ Sat, 17 Apr 2021 09:29:12: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:29:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 17 Apr 2021 09:29:18: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:29:18: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:29:18: 5000000 INFO @ Sat, 17 Apr 2021 09:29:25: 1000000 INFO @ Sat, 17 Apr 2021 09:29:25: 6000000 INFO @ Sat, 17 Apr 2021 09:29:31: 7000000 INFO @ Sat, 17 Apr 2021 09:29:31: 2000000 INFO @ Sat, 17 Apr 2021 09:29:37: 8000000 INFO @ Sat, 17 Apr 2021 09:29:37: 3000000 INFO @ Sat, 17 Apr 2021 09:29:43: 9000000 INFO @ Sat, 17 Apr 2021 09:29:43: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 09:29:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 17 Apr 2021 09:29:48: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:29:48: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:29:49: 10000000 INFO @ Sat, 17 Apr 2021 09:29:49: 5000000 INFO @ Sat, 17 Apr 2021 09:29:55: 1000000 INFO @ Sat, 17 Apr 2021 09:29:55: 11000000 INFO @ Sat, 17 Apr 2021 09:29:55: 6000000 INFO @ Sat, 17 Apr 2021 09:30:01: 7000000 INFO @ Sat, 17 Apr 2021 09:30:01: 2000000 INFO @ Sat, 17 Apr 2021 09:30:01: 12000000 INFO @ Sat, 17 Apr 2021 09:30:07: 8000000 INFO @ Sat, 17 Apr 2021 09:30:07: 3000000 INFO @ Sat, 17 Apr 2021 09:30:08: 13000000 INFO @ Sat, 17 Apr 2021 09:30:12: #1 tag size is determined as 103 bps INFO @ Sat, 17 Apr 2021 09:30:12: #1 tag size = 103 INFO @ Sat, 17 Apr 2021 09:30:12: #1 total tags in treatment: 6667322 INFO @ Sat, 17 Apr 2021 09:30:12: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:30:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:30:12: #1 tags after filtering in treatment: 2004856 INFO @ Sat, 17 Apr 2021 09:30:12: #1 Redundant rate of treatment: 0.70 INFO @ Sat, 17 Apr 2021 09:30:12: #1 finished! INFO @ Sat, 17 Apr 2021 09:30:12: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:30:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:30:12: #2 number of paired peaks: 136 WARNING @ Sat, 17 Apr 2021 09:30:12: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 17 Apr 2021 09:30:12: start model_add_line... INFO @ Sat, 17 Apr 2021 09:30:12: start X-correlation... INFO @ Sat, 17 Apr 2021 09:30:12: end of X-cor INFO @ Sat, 17 Apr 2021 09:30:12: #2 finished! INFO @ Sat, 17 Apr 2021 09:30:12: #2 predicted fragment length is 4 bps INFO @ Sat, 17 Apr 2021 09:30:12: #2 alternative fragment length(s) may be 4,10,49,597 bps INFO @ Sat, 17 Apr 2021 09:30:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.05_model.r WARNING @ Sat, 17 Apr 2021 09:30:12: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:30:12: #2 You may need to consider one of the other alternative d(s): 4,10,49,597 WARNING @ Sat, 17 Apr 2021 09:30:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:30:12: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:30:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:30:13: 9000000 INFO @ Sat, 17 Apr 2021 09:30:14: 4000000 INFO @ Sat, 17 Apr 2021 09:30:16: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:30:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:30:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:30:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.05_summits.bed INFO @ Sat, 17 Apr 2021 09:30:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:30:19: 10000000 INFO @ Sat, 17 Apr 2021 09:30:20: 5000000 INFO @ Sat, 17 Apr 2021 09:30:25: 11000000 INFO @ Sat, 17 Apr 2021 09:30:26: 6000000 INFO @ Sat, 17 Apr 2021 09:30:31: 12000000 INFO @ Sat, 17 Apr 2021 09:30:32: 7000000 INFO @ Sat, 17 Apr 2021 09:30:38: 13000000 INFO @ Sat, 17 Apr 2021 09:30:38: 8000000 INFO @ Sat, 17 Apr 2021 09:30:41: #1 tag size is determined as 103 bps INFO @ Sat, 17 Apr 2021 09:30:41: #1 tag size = 103 INFO @ Sat, 17 Apr 2021 09:30:41: #1 total tags in treatment: 6667322 INFO @ Sat, 17 Apr 2021 09:30:41: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:30:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:30:41: #1 tags after filtering in treatment: 2004856 INFO @ Sat, 17 Apr 2021 09:30:41: #1 Redundant rate of treatment: 0.70 INFO @ Sat, 17 Apr 2021 09:30:41: #1 finished! INFO @ Sat, 17 Apr 2021 09:30:41: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:30:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:30:41: #2 number of paired peaks: 136 WARNING @ Sat, 17 Apr 2021 09:30:41: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 17 Apr 2021 09:30:41: start model_add_line... INFO @ Sat, 17 Apr 2021 09:30:41: start X-correlation... INFO @ Sat, 17 Apr 2021 09:30:41: end of X-cor INFO @ Sat, 17 Apr 2021 09:30:42: #2 finished! INFO @ Sat, 17 Apr 2021 09:30:42: #2 predicted fragment length is 4 bps INFO @ Sat, 17 Apr 2021 09:30:42: #2 alternative fragment length(s) may be 4,10,49,597 bps INFO @ Sat, 17 Apr 2021 09:30:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.10_model.r WARNING @ Sat, 17 Apr 2021 09:30:42: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:30:42: #2 You may need to consider one of the other alternative d(s): 4,10,49,597 WARNING @ Sat, 17 Apr 2021 09:30:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:30:42: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:30:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:30:44: 9000000 INFO @ Sat, 17 Apr 2021 09:30:45: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:30:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:30:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:30:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.10_summits.bed INFO @ Sat, 17 Apr 2021 09:30:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:30:50: 10000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:30:56: 11000000 INFO @ Sat, 17 Apr 2021 09:31:02: 12000000 INFO @ Sat, 17 Apr 2021 09:31:08: 13000000 INFO @ Sat, 17 Apr 2021 09:31:11: #1 tag size is determined as 103 bps INFO @ Sat, 17 Apr 2021 09:31:11: #1 tag size = 103 INFO @ Sat, 17 Apr 2021 09:31:11: #1 total tags in treatment: 6667322 INFO @ Sat, 17 Apr 2021 09:31:11: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:31:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:31:12: #1 tags after filtering in treatment: 2004856 INFO @ Sat, 17 Apr 2021 09:31:12: #1 Redundant rate of treatment: 0.70 INFO @ Sat, 17 Apr 2021 09:31:12: #1 finished! INFO @ Sat, 17 Apr 2021 09:31:12: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:31:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:31:12: #2 number of paired peaks: 136 WARNING @ Sat, 17 Apr 2021 09:31:12: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 17 Apr 2021 09:31:12: start model_add_line... INFO @ Sat, 17 Apr 2021 09:31:12: start X-correlation... INFO @ Sat, 17 Apr 2021 09:31:12: end of X-cor INFO @ Sat, 17 Apr 2021 09:31:12: #2 finished! INFO @ Sat, 17 Apr 2021 09:31:12: #2 predicted fragment length is 4 bps INFO @ Sat, 17 Apr 2021 09:31:12: #2 alternative fragment length(s) may be 4,10,49,597 bps INFO @ Sat, 17 Apr 2021 09:31:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.20_model.r WARNING @ Sat, 17 Apr 2021 09:31:12: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:31:12: #2 You may need to consider one of the other alternative d(s): 4,10,49,597 WARNING @ Sat, 17 Apr 2021 09:31:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:31:12: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:31:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:31:16: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:31:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:31:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:31:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555065/SRX4555065.20_summits.bed INFO @ Sat, 17 Apr 2021 09:31:17: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling